All File Changes

v306_preview to v306_preview2 (2014-09-08 to 2014-09-15) v306

• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 73, context: html, text, full: html, text
    fix hgHubConnect to deal with bad hubs less confusing by staying inhgHubConnect if connecting to the hub fails. #13992
    
• src/hg/hgTracks/variation.c
  • lines changed 20, context: html, text, full: html, text
    Changes to snpNcbiToUcsc to handle b141 on hg19 and hg38:- When checking range{I,D,S}* locTypes, use strlen(refNCBI) as length only if
    refNCBI contains only nucleotides.
    - Checking for overlapping variants at the same location (checkCluster ->
    DuplicateObserved, MixedObserved) used to be limited to insertions because
    those are easier to check. Now we check all variants that have
    all-nucleotide observed. Libified some code from hgTracks that can
    reverse-complement a slash-separated string of alleles, e.g. G/T -> A/C,
    -/AG -> -/CT.
    - SNP IDs are getting too huge (and sparse) to use as indexes into a
    statically allocated array; use a hash.
    - Erroneous NULL frequencies in dbSNP's SNPAlleleFreq need to be detected
    and ignored.
    refs #13309
    
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 64, context: html, text, full: html, text
    Removing dead code for "useTarg" (#ifndef'd out with BRANEY_SAYS_USETARG_IS_OBSOLETE).
• src/hg/hgc/hgc.c
  • lines changed 3, context: html, text, full: html, text
    fix crash in output of predicted mRNA from geneid track #13861
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    Changing release name for taeGut2 based on user feedback, refs #13983
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 2, context: html, text, full: html, text
    Corrections based on code review, refs #13964
• src/hg/htdocs/goldenPath/help/hubQuickStart.html
  • lines changed 1, context: html, text, full: html, text
    Correcting html title, code review refs #13963
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    Changes to news to remove www.genome.ucsc.edu to genome.ucsc.edu
  • lines changed 1, context: html, text, full: html, text
    Corrections based on code review, refs #13964
• src/hg/htdocs/images/Bundibugyo_ebolavirus.jpg
  • lines changed 0, context: html, text, full: html, text
    from wikimedia commons CDC Public Health Image Library 10816
• src/hg/htdocs/images/Ebola_virus.jpg
  • lines changed 0, context: html, text, full: html, text
    generic ebola virus photo refs #13996
• src/hg/htdocs/images/Marburg_virus.jpg
  • lines changed 0, context: html, text, full: html, text
    adding marVir1 refs #13996
• src/hg/htdocs/images/Reston_ebolavirus.jpg
  • lines changed 0, context: html, text, full: html, text
    adding resEbo1 refs #13995
• src/hg/htdocs/images/Sudan_ebolavirus.jpg
  • lines changed 0, context: html, text, full: html, text
    adding sudEbo1 refs #13994
• src/hg/htdocs/images/Tai_Forest_ebolavirus.jpg
  • lines changed 0, context: html, text, full: html, text
    adding taiEbo1 refs #13997
• src/hg/htdocs/images/Zaire_ebolavirus.jpg
  • lines changed 0, context: html, text, full: html, text
    adding zaiEbo1 refs #13996
• src/hg/htdocs/images/phylo/eboVir2_49way.png
  • lines changed 0, context: html, text, full: html, text
    adding initial eboVir2 49-way tree diagram refs #13996
  • lines changed 0, context: html, text, full: html, text
    better 49-way diagram eboVir2 refs #1396
• src/hg/htdocs/indexNews.html
  • lines changed 2, context: html, text, full: html, text
    Changes to news to remove www.genome.ucsc.edu to genome.ucsc.edu
  • lines changed 1, context: html, text, full: html, text
    Corrections based on code review, refs #13964
• src/hg/inc/hubConnect.h
  • lines changed 4, context: html, text, full: html, text
    fix hgHubConnect to deal with bad hubs less confusing by staying inhgHubConnect if connecting to the hub fails. #13992
    
• src/hg/inc/trackHub.h
  • lines changed 1, context: html, text, full: html, text
    fix hgHubConnect to deal with bad hubs less confusing by staying inhgHubConnect if connecting to the hub fails. #13992
    
• src/hg/lib/bigGenePred.c
  • lines changed 5, context: html, text, full: html, text
    get genePredToBigGenePred to work with simple genePred
  • lines changed 4, context: html, text, full: html, text
    add exonFrames to genePreds that don't have them. #13861
• src/hg/lib/customFactory.c
  • lines changed 1, context: html, text, full: html, text
    strip tabs out of custom track descriptions because they confuse thejavaScript #13976
    
• src/hg/lib/hubConnect.c
  • lines changed 11, context: html, text, full: html, text
    fix hgHubConnect to deal with bad hubs less confusing by staying inhgHubConnect if connecting to the hub fails. #13992
    
• src/hg/lib/hui.c
  • lines changed 36, context: html, text, full: html, text
    Removing dead code for "useTarg" (#ifndef'd out with BRANEY_SAYS_USETARG_IS_OBSOLETE).
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    fix hgHubConnect to deal with bad hubs less confusing by staying inhgHubConnect if connecting to the hub fails. #13992
    
• src/hg/makeDb/doc/bosTau8.txt
  • lines changed 164, context: html, text, full: html, text
    Added RepeatMasker, WindowMasker, CpG Islands, Genscan and CytoBand tracks; refs #13852
• src/hg/makeDb/doc/dm6.txt
  • lines changed 400, context: html, text, full: html, text
    27 way multiz done refs #4049
• src/hg/makeDb/doc/eboVir2/genePred.txt
  • lines changed 9, context: html, text, full: html, text
    some doc for genes on eboVir2
• src/hg/makeDb/doc/eboVir2/gire.txt
  • lines changed 109, context: html, text, full: html, text
    Added a couple VCF tracks from Gire et al (99 samples from 78 patients,variants called with other Zaire-clade ebola viruses).
    
• src/hg/makeDb/doc/eboVir2/multizLabels.txt
  • lines changed 84, context: html, text, full: html, text
    Added eboVir2.multiz49wayStrainNames, which is multiz49way.maf with strain names from http://epidemic.bio.ed.ac.uk/ebolavirus_sequences
• src/hg/makeDb/doc/hg19.txt
  • lines changed 531, context: html, text, full: html, text
    SNPs(141) tracks (dbSNP b141, released for both hg19 and hg38).refs #13309
    
• src/hg/makeDb/doc/hg38.txt
  • lines changed 542, context: html, text, full: html, text
    SNPs(141) tracks (dbSNP b141, released for both hg19 and hg38).refs #13309
    
• src/hg/makeDb/genbank/src/ccds/createKeys.sql
  • lines changed 28, context: html, text, full: html, text
    CCDS changed their table schemas again
• src/hg/makeDb/genbank/src/ccds/createTables.sql
  • lines changed 118, context: html, text, full: html, text
    CCDS changed their table schemas again
• src/hg/makeDb/genbank/src/ccds/ncbiSql/convertCreateTables
  • lines changed 1, context: html, text, full: html, text
    CCDS changed their table schemas again
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createKeys.sql
  • lines changed 217, context: html, text, full: html, text
    CCDS changed their table schemas again
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createTables.sql
  • lines changed 132, context: html, text, full: html, text
    CCDS changed their table schemas again
• src/hg/makeDb/schema/all.joiner
  • lines changed 12, context: html, text, full: html, text
    SNPs(141) tracks (dbSNP b141, released for both hg19 and hg38).refs #13309
    
• src/hg/makeDb/trackDb/affyExonTissues.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on rat (rn4) track description pages
• src/hg/makeDb/trackDb/balAcu/balAcu1/trackDb.ra
  • lines changed 25, context: html, text, full: html, text
    Removing extra CpG Islands supertrack entry from lower level trackDbs
• src/hg/makeDb/trackDb/blatFugu.html
  • lines changed 9, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/blatHg16.html
  • lines changed 8, context: html, text, full: html, text
    Chaging links on fugu (fr1) track description pages
• src/hg/makeDb/trackDb/chimp/panTro2/description.html
  • lines changed 52, context: html, text, full: html, text
    Changing links on chimp (panTro2) track description pages
• src/hg/makeDb/trackDb/chimp/panTro2/gold.html
  • lines changed 8, context: html, text, full: html, text
    Changing links on chimp (panTro2) track description pages
• src/hg/makeDb/trackDb/cow/bosTau8/description.html
  • lines changed 63, context: html, text, full: html, text
    Added initial bosTau8 docs; added bosTau8 to makefile; refs #13852
• src/hg/makeDb/trackDb/cow/bosTau8/gap.html
  • lines changed 31, context: html, text, full: html, text
    Added initial bosTau8 docs; added bosTau8 to makefile; refs #13852
• src/hg/makeDb/trackDb/cow/bosTau8/gold.html
  • lines changed 34, context: html, text, full: html, text
    Added initial bosTau8 docs; added bosTau8 to makefile; refs #13852
• src/hg/makeDb/trackDb/cow/bosTau8/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Added initial bosTau8 docs; added bosTau8 to makefile; refs #13852
• src/hg/makeDb/trackDb/cpgIslandGgfAndyMasked.html
  • lines changed 6, context: html, text, full: html, text
    Changing links on rat (rn4) track description pages
• src/hg/makeDb/trackDb/drosophila/bdgpGene.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/bdgpNonCoding.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/chainAnoGam1.html
  • lines changed 25, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/chainApiMel2.html
  • lines changed 24, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/chainDp2.html
  • lines changed 27, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/chainDp3.html
  • lines changed 27, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/chainDroAna1.html
  • lines changed 27, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/chainDroMoj1.html
  • lines changed 27, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/chainDroPer1.html
  • lines changed 27, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/chainDroSec1.html
  • lines changed 27, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/chainDroSim1.html
  • lines changed 24, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/chainDroVir1.html
  • lines changed 34, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/chainDroYak1.html
  • lines changed 34, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/dm1/anophelesEcores.html
  • lines changed 30, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/dm1/cytoBand.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/dm1/description.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/dm1/flyreg.html
  • lines changed 9, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/dm1/pscreen.html
  • lines changed 10, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/dm2/affyDrosDevSignal.html
  • lines changed 32, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/dm2/affyDrosDevTransfrags.html
  • lines changed 32, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/dm2/augustus.html
  • lines changed 18, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/dm2/bacEndPairs.html
  • lines changed 6, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/dm2/cytoBand.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/dm2/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/dm2/flyBaseGene.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/dm2/flyBaseNoncoding.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/dm2/flyreg2.html
  • lines changed 8, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/dm2/multiz15way.html
  • lines changed 68, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/dm2/phastConsElements15way.html
  • lines changed 50, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/dm2/picTar.html
  • lines changed 38, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/evofold.html
  • lines changed 43, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/mzDy1Dp2Ag1_phast.html
  • lines changed 91, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/netAnoGam1.html
  • lines changed 18, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/netApiMel2.html
  • lines changed 21, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/netDp2.html
  • lines changed 21, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/netDp3.html
  • lines changed 22, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/netDroAna1.html
  • lines changed 21, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/netDroMoj1.html
  • lines changed 21, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/netDroPer1.html
  • lines changed 21, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/netDroSec1.html
  • lines changed 21, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/netDroSim1.html
  • lines changed 22, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/netDroVir1.html
  • lines changed 21, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/drosophila/netDroYak1.html
  • lines changed 21, context: html, text, full: html, text
    Changing links on D. melanogaster (dm1 and dm2 ) track description pages
• src/hg/makeDb/trackDb/ebola/bunEbo1/description.html
  • lines changed 62, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #13993
  • lines changed 1, context: html, text, full: html, text
    fixup photo reference with full name refs #13993 #13994 #13995
• src/hg/makeDb/trackDb/ebola/bunEbo1/gap.html
  • lines changed 29, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #13993
• src/hg/makeDb/trackDb/ebola/bunEbo1/gold.html
  • lines changed 33, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #13993
• src/hg/makeDb/trackDb/ebola/bunEbo1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #13993
• src/hg/makeDb/trackDb/ebola/eboVir1/description.html
  • lines changed 63, context: html, text, full: html, text
    ebola virus 46 strains refs #13996
  • lines changed 2, context: html, text, full: html, text
    indicate where the list of strains are from refs #13996
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    indicate where the list of strains are from refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir1/gap.html
  • lines changed 30, context: html, text, full: html, text
    ebola virus 46 strains refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir1/gold.html
  • lines changed 33, context: html, text, full: html, text
    ebola virus 46 strains refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    ebola virus 46 strains refs #13996
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    adding chainSelf refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir2/description.html
  • lines changed 64, context: html, text, full: html, text
    now with zaiEbo1 sequence included and NC names for the five NCBI sequences refs #13996
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    adding 49-way multiz track refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir2/gap.html
  • lines changed 30, context: html, text, full: html, text
    now with zaiEbo1 sequence included and NC names for the five NCBI sequences refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir2/gireZebov.html
  • lines changed 12, context: html, text, full: html, text
    Added a couple VCF tracks from Gire et al (99 samples from 78 patients,variants called with other Zaire-clade ebola viruses).
    
• src/hg/makeDb/trackDb/ebola/eboVir2/gold.html
  • lines changed 33, context: html, text, full: html, text
    now with zaiEbo1 sequence included and NC names for the five NCBI sequences refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra
  • lines changed 103, context: html, text, full: html, text
    adding 49-way multiz track refs #13996
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    correct reference to phylo tree image refs #13996
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    extra names on the known named strains refs #13996
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    do not need the eboVir2 mention on the sGroup_Virus refs #13996
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    add frames to the multiz49way table in eboVir2
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    visual clustering to order strains refs #13996
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    visual clustering to order strains refs #13996
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    eliminate stray blank line refs #13996
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    visual clustering to order strains refs #13996
  • lines changed 1, context: html, text, full: html, text
    visual clustering to order strains refs #13996
  • lines changed 1, context: html, text, full: html, text
    visual clustering to order strains refs #13996
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    Added eboVir2.multiz49wayStrainNames, which is multiz49way.maf with strain names from http://epidemic.bio.ed.ac.uk/ebolavirus_sequences
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49wayStrainNames.ra
  • lines changed 37, context: html, text, full: html, text
    Added eboVir2.multiz49wayStrainNames, which is multiz49way.maf with strain names from http://epidemic.bio.ed.ac.uk/ebolavirus_sequences
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    changes to make multiz use frames and VCF track name tweak
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    now with zaiEbo1 sequence included and NC names for the five NCBI sequences refs #13996
  • lines changed 14, context: html, text, full: html, text
    adding 47-strain (self) chain alignments refs #13996
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    default full viz adding 47-strain (self) chain alignments refs #13996
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    added genePredictions track from blatting proteins refs #13996
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    adding 47-strain (self) chain alignments refs #13996
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    setting default viz refs #13996
  • lines changed 1, context: html, text, full: html, text
    setting default viz refs #13996
  • lines changed 2, context: html, text, full: html, text
    adding 49-way multiz track refs #13996
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    viz on self chain to hide refs #13996
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    add ncbiGene track to eboVir2 NC_002549
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    some doc for genes on eboVir2
  • lines changed 8, context: html, text, full: html, text
    remove Hiram's gene prediction track from eboVir2
  • lines changed 1, context: html, text, full: html, text
    Added eboVir2.multiz49wayStrainNames, which is multiz49way.maf with strain names from http://epidemic.bio.ed.ac.uk/ebolavirus_sequences
  • lines changed 14, context: html, text, full: html, text
    Added a couple VCF tracks from Gire et al (99 samples from 78 patients,variants called with other Zaire-clade ebola viruses).
    
  • lines changed 1, context: html, text, full: html, text
    Making gireZebov visible by default.
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    changes to make multiz use frames and VCF track name tweak
  • lines changed 7, context: html, text, full: html, text
    adding IEDB epitopes track
• src/hg/makeDb/trackDb/ebola/marVir1/description.html
  • lines changed 63, context: html, text, full: html, text
    adding marVir1 refs #13996
• src/hg/makeDb/trackDb/ebola/marVir1/gap.html
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    adding marVir1 refs #13996
• src/hg/makeDb/trackDb/ebola/marVir1/gold.html
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    adding marVir1 refs #13996
• src/hg/makeDb/trackDb/ebola/marVir1/trackDb.ra
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    adding marVir1 refs #13996
• src/hg/makeDb/trackDb/ebola/resEbo1/description.html
  • lines changed 62, context: html, text, full: html, text
    adding resEbo1 refs #13995
  • lines changed 2, context: html, text, full: html, text
    fixup assembly links refs #13994 #13995
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    fixup photo reference with full name refs #13993 #13994 #13995
• src/hg/makeDb/trackDb/ebola/resEbo1/gap.html
  • lines changed 29, context: html, text, full: html, text
    adding resEbo1 refs #13995
• src/hg/makeDb/trackDb/ebola/resEbo1/gold.html
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    adding resEbo1 refs #13995
• src/hg/makeDb/trackDb/ebola/resEbo1/trackDb.ra
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    adding resEbo1 refs #13995
• src/hg/makeDb/trackDb/ebola/sudEbo1/description.html
  • lines changed 63, context: html, text, full: html, text
    adding sudEbo1 refs #13994
  • lines changed 3, context: html, text, full: html, text
    fixup assembly links refs #13994 #13995
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    fixup photo reference with full name refs #13993 #13994 #13995
• src/hg/makeDb/trackDb/ebola/sudEbo1/gap.html
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    adding sudEbo1 refs #13994
• src/hg/makeDb/trackDb/ebola/sudEbo1/gold.html
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    adding sudEbo1 refs #13994
• src/hg/makeDb/trackDb/ebola/sudEbo1/trackDb.ra
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    adding sudEbo1 refs #13994
• src/hg/makeDb/trackDb/ebola/taiEbo1/description.html
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    adding trackDb for taiEbo1 refs #13997
• src/hg/makeDb/trackDb/ebola/taiEbo1/gap.html
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    adding trackDb for taiEbo1 refs #13997
• src/hg/makeDb/trackDb/ebola/taiEbo1/gold.html
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    adding trackDb for taiEbo1 refs #13997
• src/hg/makeDb/trackDb/ebola/taiEbo1/trackDb.ra
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    adding trackDb for taiEbo1 refs #13997
• src/hg/makeDb/trackDb/ebola/trackDb.chainNet.ra
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    adding chain tracks for 4 others to zaiEbo1 refs #13996
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    adding lastz marVir1 refs #13996
• src/hg/makeDb/trackDb/ebola/trackDb.ra
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    adding NCBI annotation track refs #13993 #13994 #13995 #13996 #13997
  • lines changed 2, context: html, text, full: html, text
    adding chain tracks for 4 others to zaiEbo1 refs #13996
• src/hg/makeDb/trackDb/ebola/zaiEbo1/description.html
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    adding trackDb for zaiEbo1 refs #13996
• src/hg/makeDb/trackDb/ebola/zaiEbo1/gap.html
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    adding trackDb for zaiEbo1 refs #13996
• src/hg/makeDb/trackDb/ebola/zaiEbo1/gold.html
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    adding trackDb for zaiEbo1 refs #13996
• src/hg/makeDb/trackDb/ebola/zaiEbo1/trackDb.ra
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    adding trackDb for zaiEbo1 refs #13996
• src/hg/makeDb/trackDb/fugu/ecoresHg16.html
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    Chaging links on fugu (fr1) track description pages
• src/hg/makeDb/trackDb/fugu/ecoresRn3.html
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    Chaging links on fugu (fr1) track description pages
• src/hg/makeDb/trackDb/fugu/fr1/genomicSuperDups.html
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    Chaging links on fugu (fr1) track description pages
• src/hg/makeDb/trackDb/fugu/gold.html
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    Chaging links on fugu (fr1) track description pages
• src/hg/makeDb/trackDb/genomicSuperDups.html
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    Changing quotes and greater than symbols to html names, refs #13580
• src/hg/makeDb/trackDb/human/chainNetOtoGar1.ra
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    now packaging chainNet composites with a script and reign in the stray chain nets on hg19 refs #10272
• src/hg/makeDb/trackDb/human/chainNetOtoGar3.ra
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    now packaging chainNet composites with a script and reign in the stray chain nets on hg19 refs #10272
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
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    now packaging chainNet composites with a script and reign in the stray chain nets on hg19 refs #10272
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    now packaging chainNet composites with a script and reign in the stray chain nets on hg19 refs #10272
• src/hg/makeDb/trackDb/human/chainNetRBestOtoGar1.ra
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    now packaging chainNet composites with a script and reign in the stray chain nets on hg19 refs #10272
• src/hg/makeDb/trackDb/human/chainNetRBestOtoGar3.ra
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    now packaging chainNet composites with a script and reign in the stray chain nets on hg19 refs #10272
• src/hg/makeDb/trackDb/human/chainNetStray.ra
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    now packaging chainNet composites with a script and reign in the stray chain nets on hg19 refs #10272
• src/hg/makeDb/trackDb/human/hg19/denisovaMethylation.html
  • lines changed 10, context: html, text, full: html, text
    Adjusments to page to get it inline with our formatting requirements, refs #13439
• src/hg/makeDb/trackDb/human/hg19/neandertalMethylation.html
  • lines changed 10, context: html, text, full: html, text
    Adjusments to page to get it inline with our formatting requirements, refs #13439
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Removing snp141Mult track from hg19/trackDb.ra... there are no Mults in hg19 snp141!refs #13309
    
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    now packaging chainNet composites with a script and reign in the stray chain nets on hg19 refs #10272
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegDnaseClusteredV3.html
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    Add HTML page for updated DNase track. refs #13490
• src/hg/makeDb/trackDb/human/hg38/description.html
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    fixup accession ID refs #11706
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    typo fix
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    Removing extra CpG Islands supertrack entry from lower level trackDbs
• src/hg/makeDb/trackDb/makefile
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    Added initial bosTau8 docs; added bosTau8 to makefile; refs #13852
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    adding bunEbo1 to the build refs #13993
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    adding sudEbo and resEbo1 to the build refs 3994 #13995
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    adding taiEbo1 zaiEbo1 to the build refs #13996 #13997
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    adding ebola virus 46 strains refs #13996
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    adding eboVir2 refs #13996
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    adding marVir1 refs #13996
• src/hg/makeDb/trackDb/ntSeqContigs.html
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    Changing links on chimp (panTro2) track description pages
• src/hg/makeDb/trackDb/ntSeqReads.html
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    Changing links on chimp (panTro2) track description pages
• src/hg/makeDb/trackDb/pig/susScr2/description.html
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    Changing links on pig (susScr2) gateway description page
• src/hg/makeDb/trackDb/rat/genotypeArrays.html
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    Changing links on rat (rn4) track description pages
• src/hg/makeDb/trackDb/rat/rn4/description.html
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    Changing links on rat (rn4) track description pages
• src/hg/makeDb/trackDb/rat/rn4/knownGenePrevious.html
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    Changing links on rat (rn4) track description pages
• src/hg/makeDb/trackDb/rat/rn4/multiz9way.html
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    Changing links on rat (rn4) track description pages
• src/hg/makeDb/trackDb/rat/rn4/phastConsElements9way.html
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    Changing links on rat (rn4) track description pages
• src/hg/makeDb/trackDb/rat/rn4/rgdGene2.html
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    Changing links on rat (rn4) track description pages
• src/hg/makeDb/trackDb/rhesus/refSeqAnno.html
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    Changing links on rhesus (rheMac2) track description pages
• src/hg/makeDb/trackDb/rhesus/rheMac2/description.html
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    Changing links on rhesus (rheMac2) track description pages
• src/hg/makeDb/trackDb/tagTypes.tab
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    adding 49-way multiz track refs #13996
• src/hg/makeDb/trackDb/wgEncodeNhgriBip.html
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    Changing links on rhesus (rheMac2) track description pages
• src/hg/makeDb/trackDb/worm/caeJap1/description.html
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    Changing links on caeJap1 track description pages
• src/hg/makeDb/trackDb/worm/caeJap1/gold.html
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    Changing links on caeJap1 track description pages
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
  • lines changed 123, context: html, text, full: html, text
    Changes to snpNcbiToUcsc to handle b141 on hg19 and hg38:- When checking range{I,D,S}* locTypes, use strlen(refNCBI) as length only if
    refNCBI contains only nucleotides.
    - Checking for overlapping variants at the same location (checkCluster ->
    DuplicateObserved, MixedObserved) used to be limited to insertions because
    those are easier to check. Now we check all variants that have
    all-nucleotide observed. Libified some code from hgTracks that can
    reverse-complement a slash-separated string of alleles, e.g. G/T -> A/C,
    -/AG -> -/CT.
    - SNP IDs are getting too huge (and sparse) to use as indexes into a
    statically allocated array; use a hash.
    - Erroneous NULL frequencies in dbSNP's SNPAlleleFreq need to be detected
    and ignored.
    refs #13309
    
• src/hg/txGene/txGeneAccession/txGeneAccession.c
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    increase the size of a buffer that holds the id name
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 101, context: html, text, full: html, text
    Changes to support dbSNP b141, released on both hg19 and hg38:- Support multiple assemblies of the same organism in a single build.
    - Support strange one-off orgDir like human_9606_b141_GRCh37p13.
    - Added 'filter' step to extract snpNNN{Common,Mult,Flagged} sets and load tables.
    - Added coding step to make snpNNNCodingDbSnp table.
    refs #13309
    
• src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c
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    get genePredToBigGenePred to work with simple genePred
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    add exonFrames to genePreds that don't have them. #13861
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • lines changed 2, context: html, text, full: html, text
    some tweaks to support the Ebola skunk project
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    oops...
• src/hg/utils/gff3ToGenePred/tests/expected/errCases1Test.out
  • lines changed 6, context: html, text, full: html, text
    some tweaks to support the Ebola skunk project
• src/hg/utils/phyloTrees/eboVir2.49way.nh
  • lines changed 49, context: html, text, full: html, text
    eboVir2 Nway trees mostly from Baize et.al 2014-04-25 NEJM and visually added extras refs #13996
• src/hg/utils/phyloTrees/eboVir2.53way.nh
  • lines changed 53, context: html, text, full: html, text
    eboVir2 Nway trees mostly from Baize et.al 2014-04-25 NEJM and visually added extras refs #13996
• src/inc/dnautil.h
  • lines changed 5, context: html, text, full: html, text
    Changes to snpNcbiToUcsc to handle b141 on hg19 and hg38:- When checking range{I,D,S}* locTypes, use strlen(refNCBI) as length only if
    refNCBI contains only nucleotides.
    - Checking for overlapping variants at the same location (checkCluster ->
    DuplicateObserved, MixedObserved) used to be limited to insertions because
    those are easier to check. Now we check all variants that have
    all-nucleotide observed. Libified some code from hgTracks that can
    reverse-complement a slash-separated string of alleles, e.g. G/T -> A/C,
    -/AG -> -/CT.
    - SNP IDs are getting too huge (and sparse) to use as indexes into a
    statically allocated array; use a hash.
    - Erroneous NULL frequencies in dbSNP's SNPAlleleFreq need to be detected
    and ignored.
    refs #13309
    
• src/lib/dnautil.c
  • lines changed 35, context: html, text, full: html, text
    Changes to snpNcbiToUcsc to handle b141 on hg19 and hg38:- When checking range{I,D,S}* locTypes, use strlen(refNCBI) as length only if
    refNCBI contains only nucleotides.
    - Checking for overlapping variants at the same location (checkCluster ->
    DuplicateObserved, MixedObserved) used to be limited to insertions because
    those are easier to check. Now we check all variants that have
    all-nucleotide observed. Libified some code from hgTracks that can
    reverse-complement a slash-separated string of alleles, e.g. G/T -> A/C,
    -/AG -> -/CT.
    - SNP IDs are getting too huge (and sparse) to use as indexes into a
    statically allocated array; use a hash.
    - Erroneous NULL frequencies in dbSNP's SNPAlleleFreq need to be detected
    and ignored.
    refs #13309
    
• src/lib/gff3.c
  • lines changed 2, context: html, text, full: html, text
    some tweaks to support the Ebola skunk project
• src/userApps/fetchKentSource.sh
  • lines changed 1, context: html, text, full: html, text
    adding hgLoadOutJoined to the fetch refs #9149
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v306 preview2 refs #13954

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• files changed: 228